View source: R/average_chr_signal.R
average_chr_signal | R Documentation |
Computes average signal (in the score
GRanges
metadata column)
genome-wide and on each chromosome (each individual sequence determined by
seqnames
).
average_chr_signal( gr, remove_cen = FALSE, genome, cen_region_length = 50000, mean_norm = FALSE, order_chrs = FALSE )
gr |
Input signal track data as a |
remove_cen |
Logical indicating whether to remove regions around
centromeres. Defaults to |
genome |
Character string indicating reference genome used to align
the data. Must be provided when
No default. |
cen_region_length |
Integer indicating the length (in bp) of the region to remove (centered on the centromere of each chromosome). Defaults to 50'000 bp. |
mean_norm |
Logical indicating whether to normalize by average
genome-wide score. This adds two columns to the dataframe (first element of
the output list): mean ratio ( |
order_chrs |
Logical indicating whether to order rows by chromosome
length (in increasing order). Defaults to |
List with two elements:
seq_avrg
Average score
on each sequence (dataframe)
genome_avrg
Average score
genome-wide (named vector)
## Not run: average_chr_signal(GRanges_object) average_chr_signal(anti_Rec8, remove_cen=TRUE, mean_norm=TRUE, order_chrs=TRUE) average_chr_signal(anti_Rec8, remove_cen=TRUE, genome = 'SK1Yue', cen_region_length=40000, mean_norm=TRUE, order_chrs=TRUE) ## End(Not run)
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